Dear Ross,
I have changed the code of psfprm.F90. But the error message still occur. I
will try to read the code and find how to overcome this problem.
Thanks your help.
Yeng-Tseng Wang
2014-05-22 11:31 GMT+08:00 Ross Walker <ross.rosswalker.co.uk>:
> Hi Yeng,
>
> It's wrapping on fixed length arrays of 256. (ancient code. :'( ). Try
> replacing all occurrences of 256 with 512 in
> $AMBERHOME/AmberTools/src/chamber/ recompile and see if that fixes it. I
> tried a quick grep and found:
>
> grep 256 *
> psfprm.F90: character(len=256), dimension(:), allocatable :: str_files
> psfprm.F90: character(len=256) ::
> outu_name,psf_filename,prmtop_filename, &
> psfprm.F90: character(len=256) :: header
> psfprm.F90: character(len=256) :: buf
> psfprm.F90: character(len=256) :: buf
>
>
> But it's late here so there may be more.
>
> Alternatively try a box size of 256x256x256 - that's probably ok accuracy
> wise here and may run faster (power of 2 is always good) than 260^3.
>
> All the best
> Ross
>
>
> On 5/21/14, 6:23 PM, "Yeng-Tseng Wang" <c00jsw00.gmail.com> wrote:
>
> >Dear all,
> >I used the chamber to transfer the crd/psf to top/crd of amber format.
> >And
> >My command is " chamber -xpsf step5_assembly.xplor.psf -crd
> >step5_assembly.pdb -p amber.top -inpcrd amber.crd -nocmap -str stream
> >toppar.str -tip3_flex -box 260 260 260" . But I got the error message,
> >this
> >message is "FATAL ERROR: Box length must be greater than 4A". I am
> >confused
> >with this message, because I have set the length of pbc is 260 x 260 x
> >260.
> >Why the error occur ?
> >Thanks for your help
> >
> >Yeng-Tseng Wang
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 22 2014 - 02:30:03 PDT
